2Q7Y

Structure of the endogenous iNKT cell ligand iGb3 bound to mCD1d

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	295	18% PEG 4000, 0.2 M ammonium citrate, 2% butanol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.941	α = 90
b = 96.224	β = 106.23
c = 77.926	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2006-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.95	40	97.9	0.06	17.9	2.7	61120	59816			26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.02	97.8		0.449	2.32	2.7	5934

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2AKR	1.95	27.91	59295	58076	1219	97.51	0.2	0.2	0.199	0.245	RANDOM	32.361

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.01		-0.03	-0.04		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.008
r_dihedral_angle_4_deg	17.047
r_dihedral_angle_3_deg	13.811
r_dihedral_angle_1_deg	4.985
r_scangle_it	3.377
r_scbond_it	2.301
r_angle_refined_deg	1.708
r_mcangle_it	1.478
r_mcbond_it	0.997
r_nbtor_refined	0.31
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.209
r_symmetry_vdw_refined	0.182
r_symmetry_hbond_refined	0.15
r_chiral_restr	0.123
r_bond_refined_d	0.015
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5950
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	288

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing